Abstract:
:It is widely accepted that evolutionary changes in conserved developmental signaling pathways play an important role in morphological evolution. However, few in silico studies were interested in tracking such changes in a signaling pathway. The Ectodysplasin (EDA) pathway provides an opportunity to fill this gap because it is involved in vertebrate skin appendage development such as scales, teeth, hair, and feathers that take an obvious part in the adaptation of species to their environment. We benefited from the large amount of genomic data now available to explore the evolution of the upstream genes of the EDA pathway. In mammals, these genes are eda (encoding 2 ligands, EDA-A1 and EDA-A2), edar (EDA-A1 receptor), edaradd (EDA receptor [EDAR] adapter), xedar (EDA-A2 receptor), and troy (a XEDAR-related receptor). We show that the evolution of EDA pathway genes combines both strongly conserved features and evolutionary shifts. These shifts are found at different signaling levels (from the ligand to intracellular signaling) and at different taxonomic levels (class, suborder, and genera). Although conserved features likely participate to the similarities found in the early development of vertebrate skin appendages, these shifts might account for innovations and specializations. Moreover, our study demonstrates that we can now benefit from the large number of sequenced vertebrate genomes to explore the evolution of specific signaling pathways and thereby to open new perspectives for developmental biology and evolutionary developmental biology.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Pantalacci S,Chaumot A,Benoît G,Sadier A,Delsuc F,Douzery EJ,Laudet Vdoi
10.1093/molbev/msn038subject
Has Abstractpub_date
2008-05-01 00:00:00pages
912-28issue
5eissn
0737-4038issn
1537-1719pii
msn038journal_volume
25pub_type
杂志文章abstract::Serum response factor (SRF) and myocyte enhancer factor 2 (MEF2) represent two types of members of the MCM1, AGAMOUS, DEFICIENS, and SRF (MADS)-box transcription factor family present in animals and fungi. Each type has distinct biological functions, which are reflected by the distinct specificities of the proteins bo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq214
更新日期:2011-01-01 00:00:00
abstract::Two longstanding issues on the molecular clock hypothesis are studied in this article. First, is there a global molecular clock in mammals? Although many authors have observed unequal rates of nucleotide substitution among mammalian lineages, some authors have proposed a global clock for all eutherians, i.e., a single...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004043
更新日期:2002-12-01 00:00:00
abstract::Reticulate species evolution, such as hybridization or introgression, is relatively common in nature. In the presence of reticulation, species relationships can be captured by a rooted phylogenetic network, and orthologous gene evolution can be modeled as bifurcating gene trees embedded in the species network. We pres...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx307
更新日期:2018-02-01 00:00:00
abstract::The plant MADS-box regulatory gene family includes several loci that control different aspects of inflorescence and floral development. Orthologs to the Arabidopsis thaliana MADS-box floral meristem genes APETALA1 and CAULIFLOWER and the floral organ identity genes APETALA3 and PISTILLATA were isolated from the congen...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026193
更新日期:1999-08-01 00:00:00
abstract::The selective constraints influencing mRNA editing in plant organelles are largely unknown. To investigate these, we compared patterns of editing between monocot and dicot mitochondrial mRNA. On average, 24% of sites that are edited form C to U in one species have been substituted during evolution by a genomic T in th...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025768
更新日期:1997-03-01 00:00:00
abstract::Repeated attempts to map the genomic basis of complex traits often yield different outcomes because of the influence of genetic background, gene-by-environment interactions, and/or statistical limitations. However, where repeatability is low at the level of individual genes, overlap often occurs in gene ontology categ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv349
更新日期:2016-04-01 00:00:00
abstract::Protein-protein interaction networks have evolved mainly through connectivity rewiring and gene duplication. However, how protein function influences these processes and how a network grows in time have not been well studied. Using protein-protein interaction data and genomic data from the budding yeast, we first exam...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi249
更新日期:2006-01-01 00:00:00
abstract::Fish mitochondrial genome (mitogenome) data form a fundamental basis for revealing vertebrate evolution and hydrosphere ecology. Here, we report recent functional updates of MitoFish, which is a database of fish mitogenomes with a precise annotation pipeline MitoAnnotator. Most importantly, we describe implementation ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy074
更新日期:2018-06-01 00:00:00
abstract::The quantitative immunological technique of micro-complement fixation (MC'F) has been routinely used during the past decade to assess evolutionary relationships among living vertebrate species. The large data base that has been generated, along with the excellent correlations between immunologically measured genetic d...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040405
更新日期:1986-09-01 00:00:00
abstract::The proportion of functional sequence in the human genome is currently a subject of debate. The most widely accepted figure is that approximately 5% is under purifying selection. In Drosophila, estimates are an order of magnitude higher, though this corresponds to a similar quantity of sequence. These estimates depend...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp299
更新日期:2010-04-01 00:00:00
abstract::A detailed assessment of the evolution and phylogenetic utility of two genes, ftsZ and wsp, was used to investigate the origin of male-killing Wolbachia, previously isolated from the ladybird Adalia bipunctata and the butterfly Acraea encedon. The analysis included almost all available sequences of B-group Wolbachia a...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026338
更新日期:2000-04-01 00:00:00
abstract::Variation in rates of molecular evolution now appears to be widespread. The demonstration that body size is correlated with rates of molecular evolution suggests that physiological and ecological factors may be involved in molecular rate variation, but large-scale comparative studies are still lacking. Here, we use co...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025864
更新日期:1998-10-01 00:00:00
abstract::Why are certain bacterial genomes so small and compact? The adaptive genome streamlining hypothesis posits that selection acts to reduce genome size because of the metabolic burden of replicating DNA. To reveal the impact of genome streamlining on cellular traits, we reduced the Escherichia coli genome by up to 20% by...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw009
更新日期:2016-05-01 00:00:00
abstract::Human DNA variation is currently a subject of intense research because of its importance for studying human origins, evolution, and demographic history and for association studies of complex diseases. A approximately 10-kb region on chromosome 1, which contains only four small exons (each <155 bp), was sequenced for 6...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003795
更新日期:2001-02-01 00:00:00
abstract::Heterotachy occurs when the relative evolutionary rates among sites are not the same across lineages. Sequence alignments are likely to exhibit heterotachy with varying severity because the intensity of purifying selection and adaptive forces at a given amino acid or DNA sequence position is unlikely to be the same in...
journal_title:Molecular biology and evolution
pub_type: 信件
doi:10.1093/molbev/msi212
更新日期:2005-11-01 00:00:00
abstract::As the relic of the ancient Champa Kingdom, the Cham people represent the major Austronesian speakers in Mainland Southeast Asia (MSEA) and their origin is evidently associated with the Austronesian diffusion in MSEA. Hitherto, hypotheses stemming mainly from linguistic and cultural viewpoints on the origin of the Cha...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq131
更新日期:2010-10-01 00:00:00
abstract::Lethality in hybrids between Drosophila melanogaster and its sibling species Drosophila simulans is caused in part by the interaction of the genes Hybrid male rescue (Hmr) and Lethal hybrid rescue (Lhr). Hmr and Lhr have diverged under positive selection in the hybridizing species. Here we test whether positive select...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn190
更新日期:2008-11-01 00:00:00
abstract::The apparent stasis in the evolution of avian chromosomes suggests that birds may have experienced relatively low rates of gene gain and loss in multigene families. To investigate this possibility and to explore the phenotypic consequences of variation in gene copy number, we examined evolutionary changes in the famil...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu341
更新日期:2015-04-01 00:00:00
abstract::Here we report the peculiarities of molecular evolution and divergence of paralogous heterochromatic clusters of the testis- expressed X-linked Stellate and Y-linked Su(Ste) tandem repeats. It was suggested that Stellate and Su(Ste) clusters affecting male fertility are the amplified derivatives of the unique euchroma...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026348
更新日期:2000-05-01 00:00:00
abstract::Mitochondrial protein translation requires interactions between transfer RNAs encoded by the mitochondrial genome (mt-tRNAs) and mitochondrial aminoacyl tRNA synthetase proteins (mt-aaRS) encoded by the nuclear genome. It has been argued that animal mt-tRNAs have higher deleterious substitution rates relative to their...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv206
更新日期:2016-01-01 00:00:00
abstract::IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficien...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa015
更新日期:2020-05-01 00:00:00
abstract::Viral genome integration provides a complex route to biological innovation that has rarely but repeatedly occurred in one of the most diverse lineages of organisms on the planet, parasitoid wasps. We describe a novel endogenous virus in braconid wasps derived from pathogenic alphanudiviruses. Limited to a subset of th...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy148
更新日期:2018-10-01 00:00:00
abstract::The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of sta...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw046
更新日期:2016-06-01 00:00:00
abstract::Here, we sequenced the 5,419,609 bp circular genome of an Enterobacter aerogenes clinical isolate that killed a patient and was resistant to almost all current antibiotics (except gentamicin) commonly used to treat Enterobacterial infections, including colistin. Genomic and phylogenetic analyses explain the discrepanc...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss236
更新日期:2013-02-01 00:00:00
abstract::Pathogen-mediated balancing selection is regarded as a key driver of host immunogenetic diversity. A hallmark for balancing selection in humans is the heterozygote advantage at genes of the human leukocyte antigen (HLA), resulting in improved HIV-1 control. However, the actual mechanism of the observed heterozygote ad...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz249
更新日期:2020-03-01 00:00:00
abstract::We show how to make appropriate likelihood ratio tests for evolutionary tree models when parameters such as edge (internodes or branches) lengths have nonnegativity constraints. In such cases, under the null model of an edge length being zero, the marginal distribution of this parameter is proven to be a "half-normal"...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026358
更新日期:2000-05-01 00:00:00
abstract::Insertions and deletions (indels) in protein-coding genes are important sources of genetic variation. Their role in creating new proteins may be especially important after gene duplication. However, little is known about how indels affect the divergence of duplicate genes. We here study thousands of duplicate genes in...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss108
更新日期:2012-10-01 00:00:00
abstract::Identification of recently gained spliceosomal introns would provide crucial evidence in the continuing debate concerning the age and evolutionary significance of introns. A previously published genomic analysis reported to have identified 122 introns that had been gained since the divergence of the nematodes Caenorha...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msl098
更新日期:2006-12-01 00:00:00
abstract::The genomes of many vertebrates show a characteristic heterogeneous distribution of GC content, the so-called GC isochore structure. The origin of isochores has been explained via the mechanism of GC-biased gene conversion (gBGC). However, although the isochore structure is declining in many mammalian genomes, the het...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst067
更新日期:2013-07-01 00:00:00
abstract::Sequence variation among 10 alleles of the alcohol dehydrogenase (Adh) gene of the Hawaiian drosophilid D. mimica was analyzed with reference to the evolutionary history of the Hawaiian subgroup as well as to levels and patterns of polymorphism of the Adh gene in continental drosophilid species. The Adh gene of D. mim...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025582
更新日期:1996-12-01 00:00:00